eu.isas.peptideshaker.fileimport

Class PsmImporter

java.lang.Object

eu.isas.peptideshaker.fileimport.PsmImporter

public class PsmImporter
extends Object

This class can be used to import PSMs from search engine results.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsmImporter() Constructor.

Method Summary

Modifier and Type	Method and Description
HashSet<Integer>	getCharges() Returns the different charges found.
double	getMaxPeptideErrorDa() Returns the maximal peptide mass error found in Da.
double	getMaxPeptideErrorPpm() Returns the maximal peptide mass error found in ppm.
double	getMaxTagErrorDa() Returns the maximal tag mass error found in Da.
double	getMaxTagErrorPpm() Returns the maximal tag mass error found in ppm.
int	getMissingProteins() Returns the number of PSMs where a protein was missing.
int	getModificationIssue() Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
long	getnPeptideAssumptionsTotal() Returns the total number of peptide assumptions parsed.
long	getnPSMs() Returns the number of PSMs processed.
int	getnRetained() Returns the number of PSMs retained after filtering.
int	getPeptideIssue() Returns the number of PSMs which did not pass the import filters due to a peptide issue.
int	getPrecursorIssue() Returns the number of PSMs which did not pass the import filters due to a precursor issue.
HashMap<String,Integer>	getProteinCount() Returns the occurrence of each protein.
int	getProteinIssue() Returns the number of PSMs which did not pass the import filters due to a protein issue.
int	getPsmsRejected() Returns the number of PSMs which did not pass the import filters.
void	importPsms(ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, com.compomics.util.experiment.io.identification.IdfileReader fileReader, File idFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Imports PSMs.
static void	verifyXTandemModifications(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters) Verifies that the modifications targeted by the quick acetyl and quick pyrolidone are included in the identification parameters.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PsmImporter

public PsmImporter()

Constructor.

Method Detail

importPsms

public void importPsms(ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches,
                       com.compomics.util.experiment.identification.Identification identification,
                       com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                       InputMap inputMap,
                       com.compomics.util.experiment.io.identification.IdfileReader fileReader,
                       File idFile,
                       com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                       com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                       com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper,
                       int nThreads,
                       com.compomics.util.waiting.WaitingHandler waitingHandler,
                       com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                throws InterruptedException,
                       TimeoutException

Imports PSMs.

Parameters:

spectrumMatches - The PSMs to import.

identification - The identification object.

identificationParameters - The identification parameters.

inputMap - The input map.

fileReader - The file reader.

idFile - The identification file.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

fastaMapper - The sequence mapper.

nThreads - The number of threads to use.

waitingHandler - The waiting handler to display progress and allow canceling the import.

exceptionHandler - The handler of exceptions.

Throws:

InterruptedException - Exception thrown if a thread is interrupted.

TimeoutException - Exception thrown if the process timed out.

verifyXTandemModifications

public static void verifyXTandemModifications(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)

Verifies that the modifications targeted by the quick acetyl and quick pyrolidone are included in the identification parameters.

Parameters:

identificationParameters - the identification parameters

getnPSMs

public long getnPSMs()

Returns the number of PSMs processed.

Returns:

the number of PSMs processed

getnPeptideAssumptionsTotal

public long getnPeptideAssumptionsTotal()

Returns the total number of peptide assumptions parsed.

Returns:

the total number of peptide assumptions parsed

getPsmsRejected

public int getPsmsRejected()

Returns the number of PSMs which did not pass the import filters.

Returns:

the number of PSMs which did not pass the import filters

getProteinIssue

public int getProteinIssue()

Returns the number of PSMs which did not pass the import filters due to a protein issue.

Returns:

the number of PSMs which did not pass the import filters due to a protein issue

getPeptideIssue

public int getPeptideIssue()

Returns the number of PSMs which did not pass the import filters due to a peptide issue.

Returns:

the number of PSMs which did not pass the import filters due to a peptide issue

getPrecursorIssue

public int getPrecursorIssue()

Returns the number of PSMs which did not pass the import filters due to a precursor issue.

Returns:

the number of PSMs which did not pass the import filters due to a precursor issue

getModificationIssue

public int getModificationIssue()

Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.

Returns:

the number of PSMs which did not pass the import filters due to a modification parsing issue

getMissingProteins

public int getMissingProteins()

Returns the number of PSMs where a protein was missing.

Returns:

the number of PSMs where a protein was missing

getnRetained

public int getnRetained()

Returns the number of PSMs retained after filtering.

Returns:

the number of PSMs retained after filtering

getCharges

public HashSet<Integer> getCharges()

Returns the different charges found.

Returns:

the different charges found

getMaxPeptideErrorPpm

public double getMaxPeptideErrorPpm()

Returns the maximal peptide mass error found in ppm.

Returns:

the maximal peptide mass error found in ppm

getMaxPeptideErrorDa

public double getMaxPeptideErrorDa()

Returns the maximal peptide mass error found in Da.

Returns:

the maximal peptide mass error found in Da

getMaxTagErrorPpm

public double getMaxTagErrorPpm()

Returns the maximal tag mass error found in ppm.

Returns:

the maximal tag mass error found in ppm

getMaxTagErrorDa

public double getMaxTagErrorDa()

Returns the maximal tag mass error found in Da.

Returns:

the maximal tag mass error found in Da

getProteinCount

public HashMap<String,Integer> getProteinCount()

Returns the occurrence of each protein.

Returns:

the occurrence of each protein